Usages Principles

This section is used to give the principles for using our RNA-FM packages.

1. Embedding Extraction.

python launch/predict.py --config="pretrained/extract_embedding.yml" \
--data_path="./data/examples/example.fasta" --save_dir="./resuts" \
--save_frequency 1 --save_embeddings

RNA-FM embeddings with shape of (L,640) will be saved in the $save_dir/representations.

2. Downstream Prediction - RNA secondary structure.

python launch/predict.py --config="pretrained/ss_prediction.yml" \
--data_path="./data/examples/example.fasta" --save_dir="./resuts" \
--save_frequency 1

The predicted probability maps will be saved in form of .npy files, and the post-processed binary predictions will be saved in form of .ct files. You can find them in the $save_dir/r-ss.

3. Online Version - RNA-FM server.

If you have any trouble with the deployment of the local version of RNA-FM, you can access its online version from this link, RNA-FM server. You can easily submit jobs on the server and download results from it afterwards, without setting up environment and occupying any computational resources.